Dear Krisztina,
See your data at:
http://q4mdfft:q4mdfft2013.cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/
login:cluster -> q4mdfft:q4mdfft2013
Your data are kept only 5 days available:
http://q4md-forcefieldtools.org/REDS/faq.php#11
Input file: a dipeptide to the PDB file format (no more P2N file):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Mol_red1.pdb
The FF lib. you are interested in:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Mol_m1/Mol_m1-o1-sm3.mol2 (central
fragment)
-> mol3 file format
. atom typing for molecular fragments
. RESP charge with correct charge equiv. for MD
. topology and fragment connection
(do not pay attention to the pol. values available)
the whole dipeptide structure (not useful in your case):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Mol_m1/Mol_m1-o1.mol2
the frcmod file generated (for FF99; other FF can be loaded instead):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Data-Default-Proj/frcmod.correspondence
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
-> empty : no missing FF parameters
leaprc (to be developed):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft
the approach can be extended to linkers, transition metal complexes,
all the elements of the periodic tables; lone pairs & extra-points can
be added:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADFADF1-0-Krisztina1/Project.config
I hope this will help you. The unique bottleneck was to prepare the
dipeptide from the central fragment you sent to the mailing list and
writing this email ;-)
regards, Francois
> the fragment that I have sent contains only the residue for which I
> would like to get the GAFF atom types and the charges, but of course
> I ran Antechamber on a tripeptide, thus capping the open valences.
> The fragment is part of a glycopeptide containing unusual amino
> acids and linkers, so want to try to model it in GAFF as well as in
> the macromolecular AMBER forcefield (02). Thank you for the links, I
> think it will take time to go through them.
> --------------------------------------------
> On Fri, 6/21/13, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
> Subject: Re: [AMBER] GAFF atom type for CO
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, June 21, 2013, 8:49 AM
>
> Dear Krisztina,
>
> Do you want to perform atom typing for a molecular
> fragment?
> For sure Antechamber will generate errors for the atoms with
> an open
> valency...
> R.E.D. Python performs atom typing for whole molecules as
> well as
> their molecular fragments. I will send you a link for
> demonstration;
> (frcmod & leaprc files are also generated).
>
> So now, I think your best bet is to build a _dipeptide_ i.e.
> cap this
> fragment with the ACE & NME chemical groups. Then,
> derive the charges
> and build the force field library(ies) for the central
> fragment (and
> may be the N-term & C-term fragments):
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
> & may be
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
>
> You could do that in global approach with R.E.D. Server:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> and even all automatically from your dipeptide:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
>
> Here a limitation in R.E.D. Server is that a computation
> is
> re-executed if a new input is generated; thus, in the global
> approach
> a given input is generated several times; with R.E.D. Python
> this will
> be far more efficient as the inputs are compared before
> execution, and
> not re-ran if found identical.
>
> Once you got the force field libraries generated by R.E.D.
> and/or
> R.E.D. Server (mol2 file format:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php)
> (or mol3 with
> R.E.D. Python http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> with the connecting atoms defined) you can manually define
> the atom
> types (using a script; See for instance the 'F-93' R.E.DD.B.
> project
> and its LEaP script:
> http://q4md-forcefieldtools.org/REDDB/projects/F-93/).
>
> Last point: do you plan to incorporate this fragment in a
> protein
> (from what I understand from the PDB file you sent)? this
> means you
> need to use a FF for proteins (FF99SB? FF03?) and not
> GAFF...
>
> regards, Francois
>
>
> > I would like to assign GAFF atom types to
> diamino-pimelic acid (DAP)
> > with Antechamber (see attahced pdb file), but the
> carbonyl carbons
> > both on the backbone and on the sidechain as assigned
> "c2"
> > atom types instead of "c". I
> embedded DAP in a tripeptide
> > to derive the atom types and tried both sqm from
> version 12 and
> > divcon from version 9, with sqm being worse
> (assigned
> > "c1"). I tried "-j
> 5" option and used -nc 1 for
> > the charge. Is there any way to force an atom type or
> what is it
> > dependent on?
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Received on Fri Jun 21 2013 - 09:30:09 PDT
